Job ID = 11240818 sra ファイルのダウンロード中... Completed: 207233K bytes transferred in 5 seconds (310296K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 5956018 spots for /home/okishinya/chipatlas/results/dm3/SRX4798866/SRR7965203.sra Written 5956018 spots for /home/okishinya/chipatlas/results/dm3/SRX4798866/SRR7965203.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:27 5956018 reads; of these: 5956018 (100.00%) were unpaired; of these: 1655444 (27.79%) aligned 0 times 3713809 (62.35%) aligned exactly 1 time 586765 (9.85%) aligned >1 times 72.21% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 765128 / 4300574 = 0.1779 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sun, 07 Oct 2018 20:49:21: # Command line: callpeak -t SRX4798866.bam -f BAM -g dm -n SRX4798866.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4798866.20 # format = BAM # ChIP-seq file = ['SRX4798866.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 07 Oct 2018 20:49:21: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:49:21: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:49:21: # Command line: callpeak -t SRX4798866.bam -f BAM -g dm -n SRX4798866.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4798866.10 # format = BAM # ChIP-seq file = ['SRX4798866.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 07 Oct 2018 20:49:21: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:49:21: # Command line: callpeak -t SRX4798866.bam -f BAM -g dm -n SRX4798866.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4798866.05 # format = BAM # ChIP-seq file = ['SRX4798866.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 07 Oct 2018 20:49:21: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:49:21: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:49:21: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:49:28: 1000000 INFO @ Sun, 07 Oct 2018 20:49:28: 1000000 INFO @ Sun, 07 Oct 2018 20:49:28: 1000000 INFO @ Sun, 07 Oct 2018 20:49:35: 2000000 INFO @ Sun, 07 Oct 2018 20:49:35: 2000000 INFO @ Sun, 07 Oct 2018 20:49:36: 2000000 INFO @ Sun, 07 Oct 2018 20:49:41: 3000000 INFO @ Sun, 07 Oct 2018 20:49:43: 3000000 INFO @ Sun, 07 Oct 2018 20:49:43: 3000000 INFO @ Sun, 07 Oct 2018 20:49:45: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:49:45: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:49:45: #1 total tags in treatment: 3535446 INFO @ Sun, 07 Oct 2018 20:49:45: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:49:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:49:45: #1 tags after filtering in treatment: 3535446 INFO @ Sun, 07 Oct 2018 20:49:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:49:45: #1 finished! INFO @ Sun, 07 Oct 2018 20:49:45: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:49:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:49:45: #2 number of paired peaks: 876 WARNING @ Sun, 07 Oct 2018 20:49:45: Fewer paired peaks (876) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 876 pairs to build model! INFO @ Sun, 07 Oct 2018 20:49:45: start model_add_line... INFO @ Sun, 07 Oct 2018 20:49:45: start X-correlation... INFO @ Sun, 07 Oct 2018 20:49:46: end of X-cor INFO @ Sun, 07 Oct 2018 20:49:46: #2 finished! INFO @ Sun, 07 Oct 2018 20:49:46: #2 predicted fragment length is 130 bps INFO @ Sun, 07 Oct 2018 20:49:46: #2 alternative fragment length(s) may be 130,592 bps INFO @ Sun, 07 Oct 2018 20:49:46: #2.2 Generate R script for model : SRX4798866.10_model.r INFO @ Sun, 07 Oct 2018 20:49:46: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:49:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:49:47: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:49:47: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:49:47: #1 total tags in treatment: 3535446 INFO @ Sun, 07 Oct 2018 20:49:47: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:49:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:49:47: #1 tags after filtering in treatment: 3535446 INFO @ Sun, 07 Oct 2018 20:49:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:49:47: #1 finished! INFO @ Sun, 07 Oct 2018 20:49:47: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:49:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:49:47: #2 number of paired peaks: 876 WARNING @ Sun, 07 Oct 2018 20:49:47: Fewer paired peaks (876) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 876 pairs to build model! INFO @ Sun, 07 Oct 2018 20:49:47: start model_add_line... INFO @ Sun, 07 Oct 2018 20:49:47: start X-correlation... INFO @ Sun, 07 Oct 2018 20:49:47: end of X-cor INFO @ Sun, 07 Oct 2018 20:49:47: #2 finished! INFO @ Sun, 07 Oct 2018 20:49:47: #2 predicted fragment length is 130 bps INFO @ Sun, 07 Oct 2018 20:49:47: #2 alternative fragment length(s) may be 130,592 bps INFO @ Sun, 07 Oct 2018 20:49:47: #2.2 Generate R script for model : SRX4798866.05_model.r INFO @ Sun, 07 Oct 2018 20:49:47: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:49:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:49:47: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:49:47: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:49:47: #1 total tags in treatment: 3535446 INFO @ Sun, 07 Oct 2018 20:49:47: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:49:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:49:47: #1 tags after filtering in treatment: 3535446 INFO @ Sun, 07 Oct 2018 20:49:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:49:47: #1 finished! INFO @ Sun, 07 Oct 2018 20:49:47: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:49:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:49:48: #2 number of paired peaks: 876 WARNING @ Sun, 07 Oct 2018 20:49:48: Fewer paired peaks (876) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 876 pairs to build model! INFO @ Sun, 07 Oct 2018 20:49:48: start model_add_line... INFO @ Sun, 07 Oct 2018 20:49:48: start X-correlation... INFO @ Sun, 07 Oct 2018 20:49:48: end of X-cor INFO @ Sun, 07 Oct 2018 20:49:48: #2 finished! INFO @ Sun, 07 Oct 2018 20:49:48: #2 predicted fragment length is 130 bps INFO @ Sun, 07 Oct 2018 20:49:48: #2 alternative fragment length(s) may be 130,592 bps INFO @ Sun, 07 Oct 2018 20:49:48: #2.2 Generate R script for model : SRX4798866.20_model.r INFO @ Sun, 07 Oct 2018 20:49:48: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:49:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:49:54: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:49:56: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:49:57: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:49:59: #4 Write output xls file... SRX4798866.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:49:59: #4 Write peak in narrowPeak format file... SRX4798866.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:49:59: #4 Write summits bed file... SRX4798866.10_summits.bed INFO @ Sun, 07 Oct 2018 20:49:59: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (251 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:50:01: #4 Write output xls file... SRX4798866.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:50:01: #4 Write peak in narrowPeak format file... SRX4798866.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:50:01: #4 Write summits bed file... SRX4798866.05_summits.bed INFO @ Sun, 07 Oct 2018 20:50:01: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (670 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:50:02: #4 Write output xls file... SRX4798866.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:50:02: #4 Write peak in narrowPeak format file... SRX4798866.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:50:02: #4 Write summits bed file... SRX4798866.20_summits.bed INFO @ Sun, 07 Oct 2018 20:50:02: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (104 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。